High-dimensional Integration of Biological Systems

Works Published in 2023

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Displaying all 16 works

Sorted by most recent date added to the index first, which may not be the same as publication date order.

2023 journal article

Maternal organophosphate flame retardant exposure alters the developing mesencephalic dopamine system in fetal rat

TOXICOLOGICAL SCIENCES, 191(2), 357–373.

By: A. Newell n, V. Kapps n, Y. Cai n, M. Rai, G. St Armour n, B. Horman n, K. Rock n, S. Witchey n, A. Greenbaum n, H. Patisaul n

author keywords: neurodevelopment; monoamine; OPFR; OPE; flame retardants; neurotransmitters; neurotoxicity; neurotoxicology; prenatal; reproductive and developmental toxicology; mesocortical dopamine system; tissue clearing light sheet microscopy.
TL;DR: Results indicate maternal exposure to OPFRs alters the development trajectory of the embryonic dopaminergic system and adds to growing evidence of OPFR developmental neurotoxicity. (via Semantic Scholar)
Source: Web Of Science
Added: February 12, 2024

2023 article

Ten years of using key characteristics of human carcinogens to organize and evaluate mechanistic evidence in IARC Monographs on the identification of carcinogenic hazards to humans: Patterns and associations

Rusyn, I., & Wright, F. A. (2023, December 23). TOXICOLOGICAL SCIENCES.

author keywords: cancer risk assessment; risk assessment; safety evaluation
TL;DR: Increased availability of systemized data streams, such as human in vitro data, would provide the basis for confident conclusions about both positive and negative associations and constitute relative contributions of various sources of weight in expert judgments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions (OpenAlex)
Source: Web Of Science
Added: January 29, 2024

2023 journal article

Association of Pseudomonas aeruginosa infection stage with lung function trajectory in children with cystic fibrosis

JOURNAL OF CYSTIC FIBROSIS, 22(5), 857–863.

By: M. Rosenfeld*, A. Faino, P. Qu, F. Onchiri, E. Blue*, J. Collaco*, W. Gordon*, R. Szczesniak* ...

author keywords: Cystic fibrosis; Pseudomonas aeruginosa; Lung function
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 16, 2024

2023 review

AI in healthcare: navigating opportunities and challenges in digital communication

[Review of ]. FRONTIERS IN DIGITAL HEALTH, 5.

By: G. Sun n & Y. Zhou n

author keywords: remote; AI solutions; telemedicine; transformative healthcare; chatbot; Trust-AI
TL;DR: This mini-review delves into the role of AI chatbots in digital health, providing a detailed exploration of their applications, benefits, challenges, and future prospects. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: January 16, 2024

2023 article

Application of Ion Mobility Spectrometry-Mass Spectrometry for Compositional Characterization and Fingerprinting of a Library of Diverse Crude Oil Samples

Cordova, A. C., Dodds, J. N., Tsai, H.-H. D., Lloyd, D. T., Roman-Hubers, A. T., Wright, F. A., … Rusyn, I. (2023, August 22). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY.

By: A. Cordova*, J. Dodds*, H. Tsai*, D. Lloyd n, A. Roman-Hubers*, F. Wright n, W. Chiu*, T. McDonald* ...

author keywords: Analytical chemistry; Environmental chemistry; Hazard; risk assessment; Mixtures; Oil spills
TL;DR: It is found that IMS-MS data has complementary advantages for fingerprinting and characterization of diverse crude oils and that the proposed polycyclic aromatic hydrocarbon (PAH) biomarkers can be used for rapid exposure characterization. (via Semantic Scholar)
Source: Web Of Science
Added: September 5, 2023

2023 journal article

Analysis of reproducibility and robustness of a renal proximal tubule microphysiological system OrganoPlate 3-lane 40 for in vitro studies of drug transport and toxicity

TOXICOLOGICAL SCIENCES.

By: C. Sakolish*, H. Moyer*, H. Tsai*, L. Ford*, A. Dickey n, F. Wright n, G. Han*, P. Bajaj* ...

author keywords: kidney; in vitro models; validation
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Web Of Science
Added: September 5, 2023

2023 journal article

Tissue clearing and three-dimensional imaging of the whole cochlea and vestibular system from multiple large-animal models

STAR PROTOCOLS, 4(2).

By: A. Moatti n, Y. Cai n, C. Li n, K. Popowski n, K. Cheng n, F. Ligler*, A. Greenbaum n

author keywords: imaged cochleae using open -source software.; several mm; larger animal inner; open -source software
TL;DR: A protocol that enables three-dimensional (3D) characterization of intact inner ears from large-animal models is presented and a pipeline to count hair cells in antibody-stained and 3D imaged cochleae using open-source software is detailed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: September 5, 2023

2023 journal article

Deep learning-based adaptive optics for light sheet fluorescence microscopy

BIOMEDICAL OPTICS EXPRESS, 14(6), 2905–2919.

TL;DR: It is shown that the application of correction using a deformable mirror greatly improves image quality and two conceptually different network architectures are compared; one that shares convolutional features and another that estimates each aberration independently. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: July 24, 2023

2023 journal article

Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams

TOXICS, 11(7).

By: A. Cordova*, W. Klaren*, L. Ford*, F. Grimm*, E. Baker*, Y. Zhou n, F. Wright n, I. Rusyn*

author keywords: UVCB; petroleum; regulatory risk assessment; read-across; ion mobility spectrometry
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 6, 2023

2023 journal article

Assessment of drug permeability through an ex vivo porcine round window membrane model

ISCIENCE, 26(6).

By: A. Moatti n, D. Silkstone n, T. Martin n, K. Abbey n, K. Hutson*, D. Fitzpatrick*, C. Zdanski*, A. Cheng*, F. Ligler*, A. Greenbaum n

TL;DR: An ex vivo porcine RWM model, similar in structure and thickness to the human RWM, is developed, which provides a straightforward approach to developing effective and non-invasive delivery methods to the inner ear. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
5. Gender Equality (Web of Science)
Source: Web Of Science
Added: June 26, 2023

2023 journal article

Bulk and mosaic deletions of Egfr reveal regionally defined gliogenesis in the developing mouse forebrain

ISCIENCE, 26(3).

By: X. Zhang n, G. Xiao n, C. Johnson n, Y. Cai n, Z. Horowitz n, C. Mennicke n, R. Coffey*, M. Haider* ...

TL;DR: Subtractive bulk ventral and dorsal forebrain deletions of Egfr uncovered significant and permanent decreases in oligodendrogenesis and myelination in the cortex and corpus callosum, and a regenerative population of gliogenic progenitors in the mouse forebrain may compensate for the missing EGFR-dependent dorsal glia in the bulk Egfr-deleted forebrain. (via Semantic Scholar)
Source: Web Of Science
Added: June 5, 2023

2023 journal article

COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains

CELL REPORTS METHODS, 3(4).

By: Y. Cai n, X. Zhang n, C. Li n, H. Ghashghaei n & A. Greenbaum n

MeSH headings : Animals; Mice; Astrocytes; Excipients; Microscopy, Fluorescence; Neurons; Prosencephalon
TL;DR: An automated workflow to map sparsely labeled neurons and astrocytes in genetically distinct mouse forebrains using mosaic analysis with double markers (MADM) is presented and the regional and subregional effects of MADM-based deletion of the epidermal growth factor receptor (EGFR) are quantitatively analyzed. (via Semantic Scholar)
Source: Web Of Science
Added: May 30, 2023

2023 article

Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two-stage composite likelihood

Ting, B. W. W., Wright, F. A., & Zhou, Y.-H. (2023, May 22). BIOMETRICAL JOURNAL.

By: B. Ting n, F. Wright n & Y. Zhou n

author keywords: heterogeneity; heteroskedasticity; multivariate statistics; precision medicine; prediction
TL;DR: A previous method for multivariate probit estimation is built upon using a two‐stage composite likelihood that exhibits favorable computational time while retaining attractive parameter estimation properties and has the potential to better leverage genomics data and provide interpretable inference for pleiotropy. (via Semantic Scholar)
Sources: ORCID, Web Of Science
Added: May 23, 2023

2023 article

A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo

Tsai, H.-H. D., House, J. S., Wright, F. A., Chiu, W. A., & Rusyn, I. (2023, April 20). TOXICOLOGICAL SCIENCES.

author keywords: transcriptomic; petroleum; grouping; dose-response; HTTr; NAMs
MeSH headings : Humans; Transcriptome; Petroleum / toxicity; Endothelial Cells; Gene Expression Profiling; Cell Line
TL;DR: This study found that two cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: May 22, 2023

2023 journal article

Genetic Modifiers of Cystic Fibrosis Lung Disease Severity

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 207(10), 1324–1333.

By: Y. Zhou*, P. Gallins*, R. Pace*, H. Dang*, M. Aksit, E. Blue*, K. Buckingham*, J. Collaco ...

author keywords: cystic fibrosis; whole-genome sequencing; lung disease severity; GWAS/TWAS; pathway analyses
MeSH headings : Humans; Cystic Fibrosis / genetics; Genome-Wide Association Study / methods; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Patient Acuity; Lung; Microtubule-Associated Proteins / genetics
TL;DR: This pre- modulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and post-modulator genetic studies and, development of novel therapeutics for CF lung disease. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 16, 2023

2023 journal article

Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations

BIOENGINEERING-BASEL, 10(2).

By: K. Song n & Y. Zhou n

author keywords: feature selection; machine learning; microbiome; random forest; support vector machine; logistic regression
TL;DR: This study developed a method for improving the generalizability and interpretability of machine learning models for predicting three different diseases (colorectal cancer, Crohn’s disease, and immunotherapy response) using nine independent microbiome datasets using random forest as the top model. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 10, 2023

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